Genetic Variant NM_052903.6:c.2839-55G>T (chr15-23003208-C-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_052903.6(TUBGCP5):c.2839-55G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 1,516,656 control chromosomes in the GnomAD database, including 20,918 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1594 hom., cov: 32)

Exomes 𝑓: 0.16 ( 19324 hom. )

Consequence

TUBGCP5
NM_052903.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.480

Variant links:

Genes affected

TUBGCP5 (HGNC:18600): (tubulin gamma complex component 5) Enables microtubule binding activity. Involved in microtubule nucleation. Located in centrosome and cytosol. Part of gamma-tubulin large complex. [provided by Alliance of Genome Resources, Apr 2022]

TUBGCP5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 15-23003208-C-A is Benign according to our data. Variant chr15-23003208-C-A is described in ClinVar as [Benign]. Clinvar id is 1180177.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBGCP5	NM_052903.6 link	c.2839-55G>T		intron_variant	Intron 20 of 22	ENST00000615383.5	NP_443135.3	Q96RT8-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
TUBGCP5	ENST00000615383.5 link	c.2839-55G>T	intron_variant	Intron 20 of 22	1	NM_052903.6	ENSP00000480316.1	Q96RT8-1
TUBGCP5	ENST00000620435.4 link	c.2839-55G>T	intron_variant	Intron 20 of 21	2		ENSP00000481853.1	Q96RT8-2
TUBGCP5	ENST00000614508.4 link	n.2839-55G>T	intron_variant	Intron 20 of 23	5		ENSP00000484566.1	A0A087X1Z1
TUBGCP5	ENST00000620238.1 link	n.470-55G>T	intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

18990

AN:

152010

Hom.:

1594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0288

Gnomad AMI

AF:

0.221

Gnomad AMR

AF:

0.0993

Gnomad ASJ

AF:

0.121

Gnomad EAS

AF:

0.0470

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.263

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.111

GnomAD4 exome

AF:

0.163

AC:

222463

AN:

1364528

Hom.:

19324

AF XY:

0.165

AC XY:

112503

AN XY:

683292

show subpopulations

Gnomad4 AFR exome

AF:

0.0254

Gnomad4 AMR exome

AF:

0.0783

Gnomad4 ASJ exome

AF:

0.121

Gnomad4 EAS exome

AF:

0.0676

Gnomad4 SAS exome

AF:

0.206

Gnomad4 FIN exome

AF:

0.253

Gnomad4 NFE exome

AF:

0.169

Gnomad4 OTH exome

AF:

0.145

GnomAD4 genome

AF:

0.125

AC:

18989

AN:

152128

Hom.:

1594

Cov.:

AF XY:

0.129

AC XY:

9623

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0287

Gnomad4 AMR

AF:

0.0990

Gnomad4 ASJ

AF:

0.121

Gnomad4 EAS

AF:

0.0469

Gnomad4 SAS

AF:

0.213

Gnomad4 FIN

AF:

0.263

Gnomad4 NFE

AF:

0.167

Gnomad4 OTH

AF:

0.112

Alfa

AF:

0.156

Hom.:

2747

Bravo

AF:

0.106

Asia WGS

AF:

0.153

AC:

530

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Jun 19, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

7.1

DANN

Benign

0.74

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over